Evolution and Paleontology Studies

Mid-Cenozoic Rhinocerotid Dispersal via the North Atlantic

The paper describes a new Early Miocene rhinocerotid species from the Canadian High Arctic and presents phylogenetic hypotheses, suggesting the North Atlantic Land Bridge was crossable for mammals longer than previously thought.

Evolution of burrowing and associated behavioral traits in Lagomorphs

This study investigates the evolution of burrowing behavior in Lagomorphs, finding it evolved multiple times independently and correlates with sociality and higher fecundity.

Deep learning for mass extinction detection on fossilized phylogenies: power, limitations, and lessons for simulation-based phylodynamic inference

This study evaluates a deep learning model for detecting mass extinctions in fossilized phylogenies, finding it slightly better than Bayesian methods but limited by simulation stochasticity and definition specificity.

Genetical and morphological variability of the greater blind mole rat Spalax microphthalmus and phylogenetic affinities of large-bodied spalacids (Rodentia, Spalacidae) with a description of Spalax lyapunovae sp. nov. from the North Caucasus

The paper describes a new species of blind mole rat, Spalax lyapunovae, based on genetic, morphological, and chromosomal analyses of S. microphthalmus across its range.

The rise, decline and fall of clades

The paper analyzes 27 radiations using a new fossilized birth-death model to show that clade diversity follows rise and decline dynamics driven by species-level processes rather than clade-level mechanisms.

Using state space models to understand trait evolution in fossil lineages

The paper applies state space models to analyze trait evolution in fossil lineages, finding that spine number in diatoms correlates with solar insolation changes.

Phylogenies can be used to predict future diversification but with limited success

The paper evaluates how well phylogenetic tip rate methods predict future diversification using fossil and extant tetrapod data, finding moderate success with some methods.

Palaeoproteomic insights into the deep roots of the cave bear lineage in Europe

This study uses palaeoproteomics to resolve the evolutionary placement of cave bears, finding Ursus dolinensis basal within the speloid lineage.

Brawn before bite in endemic Asian eutherian mammals after the end-Cretaceous extinction

This paper shows that Paleocene placental mammals in China developed high tooth size disparity early, tracked environmental changes in dental shape later, and achieved maximum dental shape-performance integration within 10 million years post-K-Pg extinction.

Trait-space disparity in fish communities spanning 380 million years from the Late Devonian to present

This study compares trait-space diversity in Late Devonian and modern fish communities, finding temporal and habitat-related variations in functional richness and species similarity.

Ancient DNA from the Toronto subway deer adds to the extinction list of North America's Ice Age megafauna

The paper uses ancient DNA from a subway deer to clarify the taxonomic status of Torontoceros hypogaeus, suggesting it may be a distinct Odocoileus species.

Microwear variability in a spatially and temporally constrained elephant population: Implications for interpreting the diets of extant and extinct proboscideans

This study compares dental microwear texture analysis (DMTA) of modern African bush elephants to fossil mammoths to infer dietary similarities and differences.

Mass Extinction Triggered the Early Radiations of Jawed Vertebrates and Relatives (Gnathostomes)

The paper shows that the Late Ordovician Mass Extinction triggered radiations of jawed vertebrates and relatives in isolated refugia, delaying their dominance for millions of years.

The comparative analysis of lineage-pair traits.

This paper develops statistical models and tools to analyze lineage-pair traits, improving the analysis of non-independent data in evolutionary biology.

Performance and Robustness of Parameter Estimation from Phylogenetic Trees Using Neural Networks

This paper introduces a neural network ensemble method for estimating diversification parameters from phylogenetic trees, showing improved performance and robustness compared to maximum likelihood estimation.

Assessing the impact of character evolution models on phylogenetic and macroevolutionary inferences from fossil data

The paper evaluates how different models of morphological evolution affect phylogenetic and macroevolutionary inferences from fossil data using Cambrian-Ordovician trilobites.

Generalists link peaks in the shifting adaptive landscape of Australia's dragon lizards

The paper investigates the adaptive landscape of Australian dragon lizards, showing that generalist habitat use facilitated rapid morphological diversification after arrival in Australia.

On the utility of Deep Learning for model classification and parameter estimation on complex diversification scenarios.

This study compares Convolutional Neural Networks and Maximum Likelihood Estimation for classifying and estimating parameters in birth-death diversification models.

The Occurrence Birth-Death Diffusion Process: Unraveling Diversification Histories with Fossils and Heterogeneous Rates

The paper introduces the Occurrence Birth-Death Diffusion process to integrate fossil data into diversification analyses, showing fossils are essential for accurate diversification rate and richness trajectory inference.

INDITEK-2.0: A Bayesian inverse eco-evolutionary modelling framework for reconstructing Phanerozoic biodiversity

INDITEK-2.0 uses Bayesian inverse modelling to estimate eco-evolutionary parameters from synthetic biodiversity data, successfully recovering true parameter values with low uncertainty.

Graph Neural Networks for Likelihood-Free Inference in Diversification Models

This paper shows that graph neural networks with a new pooling method can accurately estimate diversification parameters in complex models where likelihoods are intractable.

DeepDiveR - A software for deep learning estimation of palaeodiversity from fossil occurrences

DeepDiveR estimates palaeodiversity from fossil occurrences using deep learning, accounting for preservation biases and showing a 37% species loss in Carnivora since the Pleistocene.

Combining fossil taxa with and without morphological data improves dated phylogenetic analyses

This study combines morphological and taxonomic data to improve dated phylogenetic analyses of trilobites, resulting in more accurate divergence time estimates and stratigraphically congruent topologies.

Six million years of vole dental evolution driven by tooth development

The paper combines fossil records and developmental biology to show that vole tooth complexity increases through developmental processes, with slower transitions toward higher cusp counts.

Unveiling the tempo of molecular and morphological evolution across the Tree of Life

This study examines molecular and morphological evolution across 40 clades, finding little support for punctuated equilibria but high among-lineage rate variation in both evolution types.

The Fossilized Birth Death Process with heterogeneous diversification rates unravels the link between diversification and specialisation to a carnivorous diet in Nimravidae (Carnivoraformes)

This paper introduces F-ClaDS, a new diversification model for phylogenetic inference, and applies it to Nimravidae fossils to show hypercarnivory drives speciation but also increases extinction risk.

A 20+ Ma old enamel proteome from Canada's High Arctic reveals diversification of Rhinocerotidae in the middle Eocene-Oligocene

This paper retrieves ancient enamel protein sequences from a 21-24 Ma rhinocerotid, providing new phylogenetic insights into Rhinocerotidae diversification during the middle Eocene-Oligocene.

Locomotor Trends Among Early Mammals Illuminated by Predictors of Arboreality from the Mammalian Appendicular Skeleton

Bayesian multilevel models of 69 appendicular skeletal metrics across 236 extant mammal species predict climbing at 95% accuracy and indicate that several Mesozoic therians, including Juramaia, were terrestrial ground-dwellers.

The complex interaction between megaherbivores, climate and fire has shaped the evolution and distribution of plant spinescence across biogeographical realms

This study investigates how megaherbivores, climate, and fire influenced the evolution and distribution of spinescence in mimosoid legumes across different biogeographical regions.

Phylogram instead of chronogram when assessing the neutral evolution of a trait

The paper argues for using phylograms over chronograms when assessing neutral trait evolution, showing simulations support better model fit with phylograms for neutral traits.